Adduction of the human N-ras codon 61 sequence with (-)-(7S,8R,9R,1OS)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene: Structural refinement of the intercalated SRSR(61,2)(-)-(7S,8R,9S,10R)-N-6-[10-(7,8,9,10-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct from H-1 NMR

The structure of the (-)-(7S,8R,9S,10R)-N-6-[10-(7,8,910-tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct at X(6) Of 5'-d(CGGACXAGAAG)-3'. 5'-d(CTTCTTGTCCG)-3', derived from trans addition of the exocyclic N-6-amino group of dA to (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo [a]pyrene [(-)-DE2], was determined using molecular dynamics simulations restrained by 369 NOEs from H-1 NMR. This was named the SRSR(61,2) adduct, derived from the N-ras protooncogene at and adjacent to the nucleotides encoding amino acid 61 (underlined) of the p21 gene product. NOEs between C-5, (S,R,SR)A(6), and A(7) were disrupted, as were those between T-17 and G(18). NOEs between benzo[a]pyrene and DNA protons were localized on the two faces of the pyrenyl ring. The benzo[a]pyrene H3-H6 protons showed NOEs to T-17 CH3, while H1, H2, and H3 showed NOEs to T-17 deoxyribose; the latter protons and H4 showed NOEs to T-17 H-2',H2 '' and to T-17 H6. NOEs were observed between H11 and H12 and C-5 H1',H2',H2 ''. G(18) NIH showed NOEs to both faces of benzo[a]pyrene. Upfield shifts of 2.6 ppm for T-17 N3H and 1.8 ppm for G(18) N1H, 1 ppm for T-17 H6 and CH3, and 0.75 ppm for C-5 H5, with a smaller shift for C-5 H6, and a 1.5 ppm dispersion of the pyrenyl protons suggested that benzo[a]pyrene intercalated above the 5'-face of (S,R,S,R)A(6). Th, precision of the refined structures was monitored by pairwise root mean square deviations, which were <1.5 Angstrom; accuracy was measured by complete relaxation matrix calculations, which yielded a sixth root R factor of 8.1 x 10(-2). Interstrand stacking between the pyrenyl ring and the T-17 pyrimidine and G(18) purine rings was enhanced by the bay ring. Changes of +30 degrees and -25 degrees in buckle for C-5 . G(18) and (S,R,S,R)A(6)T(17), respectively, were calculated, as was a -40 degrees change in propeller twist for C-5 . G(18) The rise between C-5 . G(18) and (S,R,S,R)A(6) . T-17 was calculated to be 7 Angstrom. The work extended the pattern for adenine N6 benzo[a]pyrene adducts, in which the R stereochemistry at C10 predicted 5'-intercalation of the pyrenyl moiety.